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/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.QueryInterval;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.filter.IntervalFilter;
import htsjdk.samtools.filter.SamRecordFilter;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
/**
* Create an iterator over a {@link SamReader} that only returns reads that overlap one of the intervals
* in an interval list.
*
* @author [email protected]
*/
public class SamRecordIntervalIteratorFactory {
/**
* @param samReader
* @param uniqueIntervals list of intervals of interest, with overlaps merged, in coordinate order
* @param useIndex if false, do not use a BAM index even if it is present.
* @return an iterator that will be filtered so that only SAMRecords overlapping the intervals
* in uniqueIntervals will be returned. If a BAM index is available, it will be used to improve performance.
* Note however that if there are many intervals that cover a great deal of the genome, using the BAM
* index may actually make performance worse.
*/
public CloseableIterator makeSamRecordIntervalIterator(final SamReader samReader,
final List uniqueIntervals,
final boolean useIndex) {
if (!samReader.hasIndex() || !useIndex) {
final int stopAfterSequence;
final int stopAfterPosition;
if (uniqueIntervals.isEmpty()) {
stopAfterSequence = -1;
stopAfterPosition = -1;
} else {
final Interval lastInterval = uniqueIntervals.get(uniqueIntervals.size() - 1);
stopAfterSequence = samReader.getFileHeader().getSequenceIndex(lastInterval.getContig());
stopAfterPosition = lastInterval.getEnd();
}
final IntervalFilter intervalFilter = new IntervalFilter(uniqueIntervals, samReader.getFileHeader());
return new StopAfterFilteringIterator(samReader.iterator(), intervalFilter, stopAfterSequence, stopAfterPosition);
} else {
final QueryInterval[] queryIntervals = new QueryInterval[uniqueIntervals.size()];
for (int i = 0; i < queryIntervals.length; ++i) {
final Interval inputInterval = uniqueIntervals.get(i);
queryIntervals[i] = new QueryInterval(samReader.getFileHeader().getSequenceIndex(inputInterval.getContig()),
inputInterval.getStart(), inputInterval.getEnd());
}
return samReader.queryOverlapping(queryIntervals);
}
}
/**
* Halt iteration after a read is encountered that starts after the given sequence and position.
* Note that most of this code is copied from FilteringSamIterator. It would be nice just to override getNextRecord,
* but that method is called FilteringSamIterator ctor, so the stopAfter members can't be initialized before
* it is called.
* FilteringSamIterator ctor could take a boolean "advance" that would tell it whether or not to call getNextRecord
* in the ctor, so that it could be delayed in the subclass. If this pattern happens again, we should do that.
*/
private class StopAfterFilteringIterator implements CloseableIterator {
private final int stopAfterSequence;
private final int stopAfterPosition;
private final Iterator iterator;
private final SamRecordFilter filter;
private SAMRecord next = null;
private StopAfterFilteringIterator(Iterator iterator, SamRecordFilter filter,
int stopAfterSequence, int stopAfterPosition) {
this.stopAfterSequence = stopAfterSequence;
this.stopAfterPosition = stopAfterPosition;
this.iterator = iterator;
this.filter = filter;
next = getNextRecord();
}
/**
* Returns true if the iteration has more elements.
*
* @return true if the iteration has more elements. Otherwise returns false.
*/
@Override
public boolean hasNext() {
return next != null;
}
/**
* Returns the next element in the iteration.
*
* @return the next element in the iteration
* @throws java.util.NoSuchElementException
*/
@Override
public SAMRecord next() {
if (next == null) {
throw new NoSuchElementException("Iterator has no more elements.");
}
final SAMRecord result = next;
next = getNextRecord();
return result;
}
/**
* Required method for Iterator API.
*
* @throws UnsupportedOperationException
*/
@Override
public void remove() {
throw new UnsupportedOperationException("Remove() not supported by FilteringSamIterator");
}
@Override
public void close() {
CloserUtil.close(iterator);
}
protected SAMRecord getNextRecord() {
while (iterator.hasNext()) {
SAMRecord record = iterator.next();
if (record.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) return null;
else if (record.getReferenceIndex() > stopAfterSequence) return null;
else if (record.getReferenceIndex() == stopAfterSequence && record.getAlignmentStart() > stopAfterPosition) {
return null;
}
if (!filter.filterOut(record)) {
return record;
}
}
return null;
}
}
}
